What we have to learn to do, we learn by doingAristole

Welcome toBiology: A Molecular Approach

Bio 7505Professors:

JM Crisman, PhDEJ Lehning, PhD

www.ccuri.org

Lecture Block- Basic Chemistry

Basics of Quantum Mechanics

Protons, neutrons and electrons

Atomic number- total # of protons

Atomic mass- protons + neutrons- dalton is the unit of atomic mass

Potential Energy- Energy is StoredKinetic Energy- Kinetic Energy-

Energy is releasedEnergy is released

Potential Energy vs. Kinetic Energy (stored) vs. (released)

X milesCalories

For Bonds Use

Kilocalories(kcals)

Fre

e n

rg (

Fre

e n

rg ( G

)G

)

What do the words “potential” and “kinetic” mean?

Atoms store nrg and release nrg

1) Movement of electrons between nrg (energy) levels (e.g. fluorescence)

2) Forming and breaking bonds

3) Radioactive Decay- Nrg is also released when some atoms release subatomic particles

Fig. 2.3

Fig. 2.4

Radioactive Half-life

Radioactive Isotopes Decay

electrons occupy different energy levels

NucleusNucleus

K

LL

MM

Lowest nrg

Highest nrgHighest nrg

Nrg = energy

Fig. 2.5

Fig. 2.8

Fig. 2.6Nrg in nrg levels can be use to create fluorescence

Atoms can absorb energy (potential energy) and release energy (kinetic energy)

NucleusNucleus

K

LL

MM

Lowest nrg

Highest nrgHighest nrg

Nrg = energy

Absorbnrg

Release nrg

An Example

Ionic Bonds- AKA electrovalent bonds- Atoms are in close association and

electrons are donated and change the charge of the atom.

Cations- ions with positive charge (e.g. Na+)

Anions- ions with negative charge (e.g. Cl-)

Ions:

Number of electrons does not equal the number of protons…..

So there is a charge

Redox Reactions

e- can be gained and lost during chemical reactions (rxns).

Gain of e- ---reductionLoss of e- ---oxidation

LEO SAYSGER

Used for energy transfer in biochemical reactions

Redox = reduction/oxidation reactions

Bonds and Basic Reactions

Covalent bonds- pairs of electrons are shared between atoms

Strong bonds that require significant amounts of energy to break

Bonds store energy

Atoms interact to form molecules by forming bonds

These bonds take tons of nrg to form!-So cells use molecules called enzymes that make reactions go faster!

Explain the example of making a protein from amino acids

When chemical combine they form an intermediary state calleda transition state….takes a ton of energy to get there…and when achieved the transition state allows bonds to break and new bonds to form

Enzymes lower the amount of energy needed to break and reformNew bonds…they hold reactants close together andmove electrons themselves!...usually within their own molecular structures!

Chemical reactions pass through a transition stateand enzymes speed-up reactions by lowering the nrg needed to get there

+

Fre

e n

rg (

Fre

e n

rg ( G

)G

)kc

alkc

al

reactants

products

Activation nrg (Ae)-Activation nrg (Ae)-nrg needed nrg needed to get to the to get to the

transistion state from transistion state from reactant nrg levelreactant nrg level

A + B C

Enzymes are biologicalEnzymes are biologicalcatalysts thatcatalysts thatlower the Aelower the Ae

What is an enzyme?

Use the example of two amino acids!!!!!!

Besides true bonds, there are other ways atoms interact with each other

• Van der Waal forces • Hydrogen bonds (H Bonds)• Hydrophobic interactions

Low nrg associations - are like velcro

individually these interactions are weak but collectively they are very strong

Van der Waals Interactions

Within a certain radius atoms attract each other.If they get too close…they repel each other

Molecules naturally attract each other

Van der Waal Radius

Distance that atoms of a molecule will stably interact

individually these interactions are weakbut are stronger collectively

H Bonds

DIPOLE

Water (H2O) H O H

HO

H

HO

H

O and N can form Hydrogen bonds-very weak individually but collectively strong

In fact the DNA double helix is stabilized by these interactions

PolarMolecule

Hydrophobic Interactions

Hydrophobic molecules (i.e. do not interact with water…and thus

tend to interact with each other…to “drive” water out

Very important to stabilize manymolecular structures

(e.g. cell membranes, some protein structure)

What does “hydro” and “phobic” mean?